-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathconfig.ini
executable file
·288 lines (275 loc) · 5.7 KB
/
config.ini
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
# config file for PROD environ
[global]
environ=CLIA
mode=DEV
sge=True
cores=16
jobs=40
wrapperQueue=clia_intel.q
processQueue=clia_all.q
pe=pe1
SGE_ROOT=/var/lib/gridengine
workingDir=/mnt/rnd/home/psheth/BA-132_ex19del_alternate_mutation/TrovaPipe_v6.0.0_output_assaySpecificRef_mutSpecific/working_dir
outputDir=/mnt/rnd/home/psheth/BA-132_ex19del_alternate_mutation/TrovaPipe_v6.0.0_output_assaySpecificRef_mutSpecific/
ss_infer_info=1
bypassQC=True
outputBAMSTATS=False
[runQC]
Percent Clusters Failed Demux=20
[readsProcessing]
adaptersFile=data/trovSeqsToTrim.txt
primersFile=data/trovPrimersToFlag.txt
targetsFile=data/trovTargetedRegions.bed
CUTADAPT=bin/cutadapt_wrapper
FASTQ_QUAL_FILTER=bin/fastq_quality_filter
BWA=bin/bwa-0.7.12/bwa
SAMTOOLS=bin/samtools-1.3.1/samtools
BAMREADCOUNT=bin/bam-readcount
FASTQC=bin/FastQC/fastqc
COUNT=scripts/readsProcessing/generate_RAWCOUNTS_singleFastq.pl
IGVLIB=scripts/readsProcessing/igvlib.pl
IGV=bin/IGV_2.3.79/igv.sh
IGVSERVER=node-vm1
BAMSTATS=bin/BAMStats-1.25/BAMStats-1.25.jar
MAXSLEEPDELAY=30
[dataAnalysis]
std_group_qc_file=data/weighted_mean_thresholds.RData
ntc_maxreads=102465
hs_scalar=1.3
[EGFR_L858R_P]
referenceFile=ref/hg19/hg19_primary_chromosomes.fa
mtCoordsFile=data/EGFR_L858R_mutants_coords_v3.bed
countMode=1
Qmin=30
MAPQmin=20
mismatch=0.25
percentBases=100
bwaMismatchPen=1
bwaMaxGaps=5
bwaMaxGapExts=5
bwaGapOpenPen=1
bwaGapExtPen=1
minlen=2
overlap=3
threshold_c2573=20173
dist_factor_c2573=0.302
lowest_nonzero_std_level=5
reads_qc_col=TrimmedFilteredReads
minreads=610
std_group_qc_alpha=0.02
LLoQ=5.0
[EGFR_L858R_U]
referenceFile=ref/hg19/hg19_primary_chromosomes.fa
mtCoordsFile=data/EGFR_L858R_mutants_coords_v3.bed
countMode=1
Qmin=28
MAPQmin=20
mismatch=0.35
percentBases=100
bwaMismatchPen=1
bwaMaxGaps=5
bwaMaxGapExts=5
bwaGapOpenPen=1
bwaGapExtPen=1
minlen=2
overlap=3
threshold_c2573=10644
dist_factor_c2573=0.282
lowest_nonzero_std_level=5
reads_qc_col=TrimmedFilteredReads
minreads=8848
std_group_qc_alpha=0.05
LLoQ=5.0
[EGFR_T790M_P]
referenceFile=ref/hg19/hg19_primary_chromosomes.fa
mtCoordsFile=data/EGFR_T790M_mutants_coords_v3.bed
countMode=1
Qmin=30
MAPQmin=26
mismatch=0.15
percentBases=100
bwaMismatchPen=1
bwaMaxGaps=5
bwaMaxGapExts=5
bwaGapOpenPen=1
bwaGapExtPen=1
minlen=2
overlap=3
threshold_T790M=1655
dist_factor_T790M=0.185
lowest_nonzero_std_level=5
reads_qc_col=TrimmedFilteredReads
minreads=4287
std_group_qc_alpha=0.02
LLoQ=5.0
[EGFR_T790M_U]
referenceFile=ref/hg19/hg19_primary_chromosomes.fa
mtCoordsFile=data/EGFR_T790M_mutants_coords_v3.bed
countMode=1
Qmin=25
MAPQmin=20
mismatch=0.15
percentBases=100
bwaMismatchPen=1
bwaMaxGaps=5
bwaMaxGapExts=5
bwaGapOpenPen=1
bwaGapExtPen=1
minlen=2
overlap=3
threshold_T790M=3889
dist_factor_T790M=1.23
lowest_nonzero_std_level=5
reads_qc_col=TrimmedFilteredReads
minreads=22806
std_group_qc_alpha=0.05
LLoQ=5.0
[EGFR_EX19DEL_P]
referenceFile=ref/assaySpecific/EGFR_EX19DEL_REF_fullLength.fa
mtCoordsFile=data/EGFR_EX19DEL_mutants_coords_v4.bed
countMode=2
Qmin=30
MAPQmin=12
mismatch=-1
percentBases=100
bwaMismatchPen=3
bwaMaxGaps=25
bwaMaxGapExts=25
bwaGapOpenPen=1
bwaGapExtPen=0
minlen=2
overlap=3
threshold_c.2235_2249del15=238
dist_factor_c.2235_2249del15=0.0198
lowest_nonzero_std_level=5
reads_qc_col=TrimmedFilteredReads
minreads=370
std_group_qc_alpha=0.02
LLoQ=5.0
[EGFR_EX19DEL_U]
referenceFile=ref/assaySpecific/EGFR_EX19DEL_REF_fullLength.fa
mtCoordsFile=data/EGFR_EX19DEL_mutants_coords_v4.bed
countMode=2
Qmin=28
MAPQmin=12
mismatch=-1
percentBases=100
bwaMismatchPen=3
bwaMaxGaps=25
bwaMaxGapExts=25
bwaGapOpenPen=1
bwaGapExtPen=0
minlen=2
overlap=3
threshold_c.2235_2249del15=75
dist_factor_c.2235_2249del15=0.0076
lowest_nonzero_std_level=5
reads_qc_col=TrimmedFilteredReads
minreads=66
std_group_qc_alpha=0.05
LLoQ=5.0
[KRAS_G12X_P]
referenceFile=ref/hg19/hg19_primary_chromosomes.fa
mtCoordsFile=data/KRAS_G12X_mutants_coords_v3.bed
countMode=1
Qmin=28
MAPQmin=20
mismatch=0.15
percentBases=70
bwaMismatchPen=1
bwaMaxGaps=5
bwaMaxGapExts=5
bwaGapOpenPen=1
bwaGapExtPen=1
minlen=2
overlap=3
threshold_G13D=1945
threshold_G12V=4161
threshold_G12A=4096
threshold_G12D=5882
threshold_G12C=2255
threshold_G12R=8075
threshold_G12S=415
dist_factor_G13D=1.1
dist_factor_G12V=2.4
dist_factor_G12A=0.5
dist_factor_G12D=0.9
dist_factor_G12C=1.4
dist_factor_G12R=0.5
dist_factor_G12S=0.5
lowest_nonzero_std_level=5
reads_qc_col=TotalTargetReads
minreads=33
std_group_qc_alpha=0.02
LLoQ=5.0
[KRAS_G12X_U]
referenceFile=ref/hg19/hg19_primary_chromosomes.fa
mtCoordsFile=data/KRAS_G12X_mutants_coords_v3.bed
countMode=1
Qmin=30
MAPQmin=26
mismatch=0.20
percentBases=100
bwaMismatchPen=1
bwaMaxGaps=5
bwaMaxGapExts=5
bwaGapOpenPen=1
bwaGapExtPen=1
minlen=2
overlap=3
threshold_G13D=2087
threshold_G12V=3239
threshold_G12A=1228
threshold_G12D=3671
threshold_G12C=1005
threshold_G12R=5439
threshold_G12S=168
dist_factor_G13D=1.1
dist_factor_G12V=0.9
dist_factor_G12A=0.2
dist_factor_G12D=0.2
dist_factor_G12C=0.5
dist_factor_G12R=0.2
dist_factor_G12S=0.2
lowest_nonzero_std_level=5
reads_qc_col=TotalTargetReads
minreads=37
std_group_qc_alpha=0.05
LLoQ=5.0
[BRAF_V600X_P]
referenceFile=ref/hg19/hg19_primary_chromosomes.fa
mtCoordsFile=data/BRAF_V600X_mutants_coords_v3.bed
countMode=1
Qmin=25
MAPQmin=20
mismatch=0.25
percentBases=100
bwaMismatchPen=1
bwaMaxGaps=5
bwaMaxGapExts=5
bwaGapOpenPen=1
bwaGapExtPen=1
minlen=2
overlap=3
threshold_V600E=342
dist_factor_V600E=0.761
lowest_nonzero_std_level=10
reads_qc_col=TrimmedFilteredReads
minreads=88891
std_group_qc_alpha=0.02
LLoQ=5.0
[BRAF_V600X_U]
referenceFile=ref/hg19/hg19_primary_chromosomes.fa
mtCoordsFile=data/BRAF_V600X_mutants_coords_v3.bed
countMode=1
Qmin=30
MAPQmin=26
mismatch=0.0
percentBases=100
bwaMismatchPen=1
bwaMaxGaps=5
bwaMaxGapExts=5
bwaGapOpenPen=1
bwaGapExtPen=1
minlen=2
overlap=3